You can't do it through iSync, but you can still get something pretty similar in OmniWeb 4.5 beta. The current betas include an early-adopter version of a feature that'll be fleshed out post-4.5: WebDAV-based bookmarks. The implementation is quite different from Safari/iSync, but the result is the same: your bookmarks can "live" on the web, and all the machines you use them from can share them.

To enable this feature:
1. Copy your bookmarks file (by default it's in ~/Library/Application Support/OmniWeb/Bookmarks.html) to your iDisk or another WebDAV server.
2. In OmniWeb's Bookmarks preferences, set the Personal Bookmarks URL to the URL of the file on the WebDAV server. (e.g., if you put it on your iDisk, it'd be something like http://idisk.mac.com/username/Documents/Bookmarks.html)
3. Quit and restart OmniWeb.

Again, this is an early-adopter preview... before you rush to send us feedback on how unfinished it is, let me remind you that we know it's unfinished. :) A better setup UI, better timing for synchronization, and a UI for conflict resolution are all planned.